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OPENSEQ.org
DhaK_DhaL
Genes: A B A+B
Length: 354 209 536
Sequences: 2402 2899 1244
Seq/Len: 6.79 13.87 2.32
MirrorTree (Pazo et al. 2001) 0.71
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.01 2.21
2 0.07 0.06 2.26
5 0.14 0.07 2.28
10 0.14 0.07 2.30
20 0.14 0.07 2.30
100 0.14 0.07 2.31
∞ 0.16 0.09 2.31
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
121_D 92_Q 1.30 0.84 0.14
117_E 89_R 1.30 0.84 0.14
121_D 88_I 1.27 0.82 0.13
118_L 88_I 1.25 0.81 0.12
113_E 119_R 1.21 0.77 0.10
200_K 27_G 1.07 0.65 0.07
113_E 121_K 1.07 0.65 0.07
83_D 73_S 1.03 0.60 0.06
117_E 119_R 0.96 0.53 0.05
78_T 71_L 0.95 0.51 0.05
106_T 180_Y 0.95 0.51 0.04
78_T 78_A 0.94 0.49 0.04
82_P 37_H 0.90 0.45 0.04
78_T 43_R 0.87 0.42 0.03
125_K 163_S 0.83 0.37 0.03
56_E 77_G 0.82 0.36 0.03
150_A 35_A 0.81 0.35 0.03
123_G 92_Q 0.81 0.35 0.03
202_S 30_R 0.81 0.35 0.03
82_P 195_S 0.79 0.34 0.03
78_T 40_N 0.79 0.33 0.03
71_A 79_S 0.79 0.33 0.03
62_Y 79_S 0.78 0.32 0.02
290_S 81_P 0.78 0.32 0.02
81_T 51_K 0.77 0.31 0.02
113_E 78_A 0.75 0.29 0.02
75_E 43_R 0.75 0.29 0.02
103_K 180_Y 0.74 0.29 0.02
322_L 179_S 0.73 0.28 0.02
56_E 79_S 0.73 0.27 0.02
59_H 79_S 0.72 0.27 0.02
109_I 82_L 0.72 0.26 0.02
56_E 37_H 0.72 0.26 0.02
204_T 5_T 0.71 0.26 0.02
156_E 40_N 0.71 0.26 0.02
75_E 71_L 0.71 0.25 0.02
136_A 191_P 0.70 0.24 0.02
59_H 180_Y 0.70 0.24 0.02
116_T 122_A 0.70 0.24 0.02
237_M 74_S 0.70 0.24 0.02
78_T 37_H 0.70 0.24 0.02
78_T 75_V 0.69 0.24 0.02
210_M 41_M 0.69 0.23 0.02
336_D 5_T 0.69 0.23 0.02
231_D 54_A 0.68 0.23 0.02
103_K 79_S 0.68 0.23 0.02
56_E 76_G 0.68 0.23 0.02
103_K 40_N 0.68 0.23 0.02
79_S 40_N 0.68 0.23 0.02
206_A 5_T 0.67 0.22 0.02
290_S 37_H 0.67 0.22 0.01
123_G 95_Q 0.67 0.22 0.01
238_F 27_G 0.67 0.22 0.01
103_K 175_K 0.66 0.21 0.01
117_E 58_K 0.66 0.21 0.01
75_E 63_I 0.65 0.21 0.01
202_S 133_W 0.65 0.20 0.01
350_A 77_G 0.65 0.20 0.01
78_T 195_S 0.65 0.20 0.01
110_L 59_D 0.65 0.20 0.01
78_T 32_I 0.65 0.20 0.01
195_V 178_A 0.64 0.20 0.01
152_T 77_G 0.64 0.20 0.01
56_E 81_P 0.64 0.20 0.01
197_A 39_L 0.64 0.20 0.01
69_S 161_A 0.64 0.19 0.01
114_T 89_R 0.64 0.19 0.01
99_L 7_I 0.63 0.19 0.01
152_T 180_Y 0.63 0.19 0.01
70_G 90_A 0.63 0.19 0.01
132_D 199_M 0.63 0.19 0.01
180_N 42_N 0.63 0.19 0.01
71_A 173_A 0.63 0.19 0.01
81_T 81_P 0.62 0.18 0.01
205_L 30_R 0.62 0.18 0.01
317_A 23_E 0.62 0.18 0.01
212_F 23_E 0.62 0.18 0.01
145_G 180_Y 0.62 0.18 0.01
49_S 76_G 0.61 0.18 0.01
145_G 179_S 0.61 0.18 0.01
192_A 30_R 0.61 0.18 0.01
216_I 79_S 0.61 0.18 0.01
56_E 195_S 0.61 0.17 0.01
109_I 121_K 0.60 0.17 0.01
152_T 79_S 0.60 0.17 0.01
168_S 138_E 0.60 0.17 0.01
243_V 98_Q 0.60 0.17 0.01
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
5274 2.32 DhaK_DhaL Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.14 Done
5273 2.09 DhaK_DhaL Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.01 Done
5270 3.01 DhaK_DhaL Δgene:(0, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.03 Done
5269 2.41 DhaK_DhaL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.33 Done - Shared
5268 1.6 DhaK_DhaL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.06 Done - Shared
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